Methods for mixing fluid in a rotating container

ABSTRACT

The invention provides exemplary devices, systems and methods for mixing of fluids, such as biological fluids. One exemplary device comprises is particularly adapted for holding at least one cartridge having a chamber containing a biological fluid, with the chamber having a generally planar face. The device comprises a rotatable body having a rotational axis. The rotatable body includes at least one mounting element which is adapted to mount the rotatable body such that the face of the chamber is generally perpendicular to the rotational axis.

This application is a divisional of application Ser. No. 10/062,431,filed 30 Jan. 2002, now U.S. Pat. No. 6,705,754, which is a continuationof application Ser. No. 09/487,506, filed 19 Jan. 2000, now abandoned,which is a continuation of application Ser. No. 09/032,724, filed 27Feb. 1998, now U.S. Pat. No. 6,050,179, which is a continuation-in-partof application Ser. No. 09/016,564, filed 30 Jan. 1998, now abandoned,the disclosures of which applications are incorporated by reference.

BACKGROUND OF THE INVENTION

This invention relates generally to the field of mixing, and inparticular to the mixing of fluids. In one particular aspect, theinvention relates to the mixing of biological fluids within a chamberwhich is disposed within a heated environment.

Methods for using arrays of polymers to identify receptors with specificaffinities for one of the polymers in the array are known. For example,one method uses immobilized antibodies to analyze binding to peptideligands or vice-versa. Another type of method uses immobilizedoligonucleotides to analyze hybridization to a target nucleic acid. Forinstance, U.S. patent application Ser. No. 08/624,312, filed Mar. 26,1996, the complete disclosure of which is herein incorporated byreference, describes apparatus and methods for carrying out repeatedhybridizations of a target nucleic acid to an array of nucleic acidprobes. Such polymer arrays are described in, e.g., U.S. Pat. No.5,143,854 and published PCT Application Nos. WO90/15070 and WO92/10092,the complete disclosures of which are herein incorporated by reference.These polymer arrays are nucleic acid arrays which include a pluralityof different polynucleotides coupled to a substrate in different knownlocations.

In one exemplary arrangement, such arrays are packaged within a housing,like those described in, e.g., pending U.S. patent application Ser. Nos.08/624,312, previously incorporated by reference, Ser. No. 08/485,452,filed Jun. 7, 1995, and Ser. No. 08/528,173, filed Sep. 19, 1995, andpublished PCT Application No. WO95/33846. The disclosures of all ofthese references are herein incorporated by reference. In brief, such ahousing typically includes a body having a reaction cavity orhybridization chamber. The array or substrate is mounted over the cavityon the body such that the front side of the array substrate, e.g., theside upon which the polynucleotides are situated, is in fluidcommunication with the cavity. The cartridge includes inlet and outletports to allow various fluids to be introduced into and removed from thehybridization chamber.

During hybridization, it is often desirable to provide an efficient andeffective way to mix the fluids within the chamber. This can bechallenging since the chamber is typically in a temperature controlledenvironment, such as in an oven. Additionally, in at least oneembodiment, the interior of the chamber is narrow, and it can bedifficult to mix or agitate the fluid when within the chamber.

Hence, it would be desirable to provide devices, systems and methods tofacilitate the mixing of fluids which are held within a hybridizationchamber to improve the hybridization process. Such devices, systems andmethods should be cost effective, easy to use, and be compatible withthe constraints of the hybridization process. In particular, it would bedesirable if mixing of the fluid could be facilitated while the chamberis within a temperature controlled environment, such as an oven.

SUMMARY OF THE INVENTION

The invention provides systems, devices and methods for facilitating themixing of various fluids within a chamber. In one exemplary embodiment,a system is provided which comprises at least one cartridge having achamber for holding a fluid (which is preferably a biological fluid),with the chamber including a generally planar face. The system furtherincludes a rotatable body having a rotational axis. The rotatable bodyincludes at least one mounting element to removably mount the cartridgeto the rotatable body such that the face of the chamber is generallyperpendicular to the rotational axis.

In one exemplary aspect, the mounting element comprises a pair ofopposing walls which each include at least one slot. The slots arearranged such that the cartridge is insertable into the slots.Conveniently, the rotatable body may also include a base which connectsthe pair of walls. Preferably, the rotational axis extends through oneof the walls. In this way, the cartridge will be spaced apart from therotational axis to facilitate mixing of the fluid when the body isrotated.

In another aspect, the opposing walls are parallel to each other and theslots are configured such that the face of the chamber is generallyperpendicular to the walls when placed into the slots. Preferably, atleast one of the slots is keyed such that the cartridge is insertableinto the slot in only one orientation. Optionally, each wall may includea plurality of slots which are arranged such that multiple cartridgesmay be inserted into the slots in a parallel arrangement. It will beappreciated that the rotatable body may include additional numbers ofparallel walls which each include slots so that multiple cartridges maybe removably mounted to the body.

In one aspect, a lid is also provided and is operably attached to atleast one of the walls. The lid is movable between an open and a closedposition, with the lid securing the cartridge within the slots when thelid is in the closed position. At least one coupling element ispreferably operably attached to the body in alignment with therotational axis. In this way, the coupling element may couple therotatable body to a rotation mechanism.

In one particular aspect, the chamber includes a pair of planar spacedapart faces which define an interior having the fluid. The faces aregenerally rectangular or square in geometry, and the cartridge ismounted to the body such that the faces are generally perpendicular tothe rotational axis to facilitate mixing of the fluid within thechamber.

The body will preferably be rotated about the rotational axis at a ratein the range from about 30 rpm to about 90 rpm, and more preferably fromabout 50 rpm to about 60 rpm. Further, the rotational body willpreferably be placed within a temperature controlled environment duringrotation of the body. In one particular aspect, the chamber is heated toa temperature in the range from about 30° C. to about 60° C., and morepreferably from about 40° C. to about 50° C., while the body isrotating. Such heating may be accomplished, for example, by placing therotatable body within an oven.

In a preferred aspect, the device will be fabricated of transparentplexiglass or other suitable lightweight, rigid, machinable material andbe a generally amber color such that wavelengths of light in the rangeof 200 nm to 700 nm will be filtered out.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a perspective view of an exemplary device for holding multiplecartridges which each include a hybridization chamber according to theinvention.

FIG. 2 is a top view of the device of FIG. 1.

FIG. 3 is a right side view of the device of FIG. 1.

FIG. 4 is a left side view of the device of FIG. 1.

FIG. 5 is a partial cutaway view of the device of FIG. 1 showing acartridge being inserted into the device according to the invention.

FIG. 6 illustrates a method for rotating the device of FIG. 1 aftercartridges have been inserted into the device according to theinvention.

DETAIL DESCRIPTION OF THE SPECIFIC EMBODIMENTS

The invention provides exemplary devices, systems and methods tofacilitate the mixing of fluids that are held within a chamber, and willpreferably be used in connection with biological fluids. Although usefulin mixing a wide variety of biological fluids, the invention will findits greatest use when mixing a sample within a hybridization chamberhaving a polymer array. Although the invention will find particular usein connection with hybridization reactions and, more specifically,nucleic acid hybridizations, it should be appreciated that the inventionwill be useful in facilitating a variety of reactions where mixing isrequired, including, e.g., extension or amplification reactions usingtethered probes as template or primer sequences, screening of receptorsagainst arrays of small molecules, peptides or peptideomimetics,carbohydrates, and the like.

The invention will find use in facilitating the mixing of fluids withinchambers having a wide variety of configurations and geometries.However, the invention will be particularly useful with chambers whichare relatively narrow in geometry, e.g., defined by two closely spacedapart planar walls. Such chambers are described in co-pending U.S.application Ser. Nos. 08/624,312, 08/485,452 and 08/528,173 and PCTApplication No. WO95/33846, previously incorporated herein by reference.

The invention provides for the mixing of the various fluids by rotatingthe chambers about a rotational axis that is generally perpendicular tothe narrow chamber. Rotation in this manner is particularly advantageouswhen the chamber includes corners, such as in a rectangular or squarechamber.

When rotating the chamber about the rotational axis, the fluid withinthe chamber will become agitated as the direction of flow is hindereddue to the change in direction of the walls. In this way, mixing of thefluid is facilitated.

According to the invention, mixing will preferably occur while thechamber is within a temperature controlled environment. Typically, thechamber will be included within an oven so that the chamber may beheated while the chamber is being rotated. For example, one such ovenwhich may be modified to receive a rotating chamber is a General PurposeIncubator, Model 1535, commercially available from VWR ScientificProducts, West Chester, Pa.

Referring now to the figures, an exemplary embodiment of a device 10 forholding cartridges having a chamber containing a fluid will bedescribed. The fluid held within the chamber will preferably comprise abiological fluid. The cartridges will preferably be of the typedescribed generally in co-pending U.S. application Ser. Nos. 08/624,312,08/485,452 and 08/528,173 and PCT Application No. WO95/33846, previouslyincorporated by reference. Such cartridges are illustrated generally inFIG. 5 and will be described in greater detail hereinafter.

Device 10 comprises a rotational body 12 having a base 14, a pluralityof parallel spaced apart walls 16, 18 and is 20, and two end pieces 22and 24. As best shown in FIGS. 2–4, coupling elements 26 and 28 areattached to end pieces 22 and 24, respectively. Extending betweencoupling elements 26 and 28 (and through wall 18) is a rotational axisabout which body 12 is rotated as described in greater detailhereinafter.

End pieces 22 and 24 each include a set of apertures 30 as best shown inFIG. 1. Apertures 30 are employed to couple a lid 32 to end pieces 22and 24. As shown in FIG. 1, lid 32 is in an open position. In FIGS. 2–4,lid 34 is in a closed position. Lid 32 is coupled to end pieces 22 and24 by rods 34, which in turn are attached to lid 32 by brackets 36.

A spring 38 is disposed within each of brackets 36 to bias rods 34toward their respective aperture 30 so that lid 32 will be secured toend pieces 22 and 24 when in the closed position.

The elements used to construct body 12 will preferably comprise agenerally rigid, heat resistant material that may withstand temperaturesthat are within the range of from about 30° C. to about 60° C., and morepreferably from about 40° C. to about 50° C. Conveniently, the elementsused to construct body 12 comprise a plastic material, with a preferablematerial being sold under the trade name of Plexiglass. Other suitablelightweight, rigid, machinable, heat resistant materials includingacrylic, lucite, styrene, polystyrene, and polycarbonate may also beused. Conveniently, the elements may be constructed to be essentiallytransparent so that visualization into body 12 may be facilitated. In apreferred embodiment, the elements are generally amber in color suchthat wavelengths of light in the range of 200 nm to 700 nm, and morepreferably 250 nm to 600 nm, will be prevented from passingtherethrough.

As best shown in FIG. 3, coupling element 26 includes a cylindrical hole40 which is aligned with the rotational axis. Hole 40 is adapted toreceive a rotatable shaft so that, as the shaft is rotated, body 12 willrotate about the rotational axis. As shown in FIG. 2, coupling element28 includes a rotatable sleeve 42 which is adapted to rest upon abracket (not shown) so that body 12 will rotate about the rotationalaxis when the shaft in hole 40 is rotated. An exemplary motor unit forrotating body 12 comprises a Rotamix Rotisserie with Digital Display,commercially available from Appropriate Technical Resources, Laurel Md.Preferably, body 12 is coupled to the motor unit, and the motor unit isthen placed into the oven or incubator. The motor unit is then actuatedto rotate body 12 within the oven.

Referring now to FIGS. 1 and 2, walls 16 and 20 each include a pluralityof slots 44. Slots 44 in each of walls 16 and 20 oppose a correspondingslot 46 in wall 18. In this way, a cartridge 48 (see FIG. 5) may beremovably mounted to body 12 by inserting the cartridge between a pairof opposing slots 44 and 46. Conveniently, a pair of cross walls 50 areprovided to subdivide body 12 into four sections. The division of body12 into various sections facilitates organization of the variouscartridges.

Each pair of opposing slots 44 and 46 are configured such that when thecartridge is inserted into the slots, the cartridge will be generallyperpendicular to walls 16, 18 and 20. As described hereinafter, slots 46are narrower than slots 44 so that the cartridges can only be insertedin one particular orientation. Conveniently, lid 32 is provided with apair of rubber strips 52 which serve to securely hold the cartridgewithin slots 44 and 46 when lid 32 is in the closed position.

Referring now to FIG. 5, insertion of cartridges 48 into body 12 will bedescribed in greater detail. The particular construction of cartridge 48is described in co-pending U.S. application Ser. Nos. 08/624,312,08/485,452 and 08/528,173 and PCT Application No. WO95/33846, previouslyincorporated by reference. Briefly, cartridge 48 includes a front 54 anda rear 56. Front 54 includes a cavity 58 which is defined by a generallyplanar face 60. Positioned across cavity 58 is an array chip (notshown). When the array chip is positioned over cavity 58, ahybridization chamber is formed. The hybridization chamber is generallyrectangular or square in geometry and has a narrow width as defined bythe distance between planar face 60 and the array chip. An inlet port 62and an outlet port 64 are included in rear 56 to allow various fluids tobe introduced into and removed from the hybridization chamber. Rear 56further includes a cavity 66, located adjacent the array, which isadapted for receiving a temperature monitoring and/or controlling deviceemployed in other applications.

Cartridge 48 includes an extending edge 68 which is sized to be receivedinto slots 46, while the opposite side of cartridge 48 is adapted to bereceived in slots 44. In this way, cartridge 48 can only be insertedbetween a pair of slots 44 and 46 in one orientation as shown in FIG. 5.In such an orientation, planar face 60 is generally perpendicular to therotational axis. In this way, as body 12 is rotated, the fluid withinthe hybridization chamber will flow against each edge of thehybridization chamber to facilitate mixing of the fluid.

Referring now to FIGS. 5 and 6, operation of device 10 to facilitatemixing of a fluid, such as a biological fluid, will be described.Initially, the hybridization chamber within cartridge 48 is at leastpartially filled with a liquid. Cartridge 48 is then inserted between apair of opposing slots 44 and 46, with edge 68 being inserted into slot46. Lid 32 is then closed, with each of rods 34 being received into itsrespective aperture 30. Strips 52 will be pressed upon cartridge 48 tosecurely hold the cartridges within the slots. Device 10 is then coupledto a rotation unit and placed within an oven as previously described.The oven is set to the desired temperature, which will typically be inthe range from about 30° C. to about 60° C., and more preferably fromabout 40° C. to about 50° C. While within the oven, the rotationmechanism is actuated to rotate body 12 about the rotational axis asillustrated by the arrow in FIG. 6. Preferably, body 12 will be rotatedat a rate in the range from about 30 rpm to about 90 rpm, and morepreferably from about 50 rpm to about 60 rpm.

After mixing and heating is completed, device 10 is removed from theoven and lid 32 is opened so that cartridges 48 may be removed. At thispoint, cartridges 48 may be processed further as is known in the art.

While the foregoing invention has been described in some detail forpurposes of clarity and understanding, it will be clear to one skilledin the art from a reading of this disclosure that various changes inform and detail can be made without departing from the true scope of theinvention. All publications are incorporated by reference in theirentirety for all purposes to the same extent as if each individualpublication or patent documents were so individually denoted regardlessof whether previously incorporated by reference.

1. A method for facilitating the mixing of a fluid, the methodcomprising: providing a container containing a polymer array havingcomplementary probe sequences and a fluid containing at least one targetmolecule; coupling the container to a holding device comprising arotational axis, a pair of end members extending from the rotationalaxis and a plurality of walls extending between the end members parallelto the rotational axis, such that the polymer array is substantiallyperpendicular to the rotational axis; and rotating the holding deviceabout the rotational axis such that the fluid is agitated to mix thefluid within the container.
 2. A method as in claim 1, wherein: theholding device further comprises a first pair of rails fixedly attachedto a first wall to form a first slot and a second pair of rails fixedlyattached to a second wall to form a second slot; the container furthercomprises a first end and a second end; and coupling the container tothe holding device comprises removably positioning the first end in thefirst slot and removably positioning the second end in the second slot.3. A method as in claim 1, wherein the container defines a chamber, thechamber including a pair of closely spaced-apart faces that areseparated by walls to define a narrow interior, wherein one of the facesdefines a planar surface on which the probe array is disposed.
 4. Amethod as in claim 3, wherein the walls of the chamber are set at anglessufficient to agitate the fluid when rotated.
 5. A method as in claim 1,further comprising rotating the body about the rotational axis at a ratein the range from about 30 rpm to about 90 rpm.
 6. A method forfacilitating the mixing of a fluid, the method comprising: providing anoven having an open interior; providing a container containing a polymerarray and a fluid; coupling the container to a holding device comprisinga rotational axis, a pair of end members extending from the rotationalaxis and one or more walls extending between the end members parallel tothe rotational axis, such that the polymer array is substantiallyperpendicular to the rotational axis; and rotatably positioning theholding device within the interior of the oven and rotating the holdingdevice about the rotational axis such that the fluid is agitated to mixthe fluid within the container; and supplying heat to the interior ofthe oven while rotating the holding device.
 7. A method as in claim 6,wherein the container defines a chamber, the chamber including a pair ofclosely spaced-apart faces that are separated by walls to define anarrow interior, wherein one of the faces defines a planar surface onwhich the polymer array is disposed.
 8. A method as in claim 7, whereinthe walls of the chamber are set at angles sufficient to agitate thefluid when rotated.